Republic of the Philippines

Surigao Del Sur State University

TAGBINA CAMPUS
Tagbina, Surigao del Sur 8300
Email address: [email protected]
Website: www.sdssu.edu.ph

LEARNING MODULE
in
GENERAL
BIOCHEMISTRY
(CHEM. 2)

NAME : ————————————————

PROGRAM/YEAR LEVEL : ————————————————

INSTRUCTOR : ————————————————

SEMESTER : ————————————————
SCHOOL YEAR : ————————————————

Compiled by:

DEMEIAPE V. BAGALAY
Course Instructor
 Republic of the Philippines

Surigao Del Sur State University

TAGBINA CAMPUS
Tagbina, Surigao del Sur 8300
Email address: [email protected]
Website: www.sdssu.edu.ph

VISION
A leading ―Glocal‖ University with widened academic perspectives that focus on attaining
food security, supporting poverty alleviation, developing renewable energy, and conserving
natural environment

MISSION
SDSSU shall provide competency based higher education and training driven by relevant
and responsive instruction, research, extension and sustainable resource management.

PROGRAM GOALS:

The College of Agricultural Sciences and Technology aims to:

1. Produce quality and relevant education and training within the reach of the low-income
members of society
2. Provide students with entrepreneurial skills and trainings in the agri-business, commer-
cial sciences, information technology and
3. Produce graduates equipped with the necessary values, attitudes, knowledge and skills.

PROGRAM INTENDED LEARNING OUTCOMES:

Specific Program Outcomes - Bachelor in Agricultural Technology (BAT) Program:

1. Exhibit comprehensive knowledge of various learning areas in Bachelor of Agricultural
Technology curriculum
2. Execute techniques, skills and utilize modern tools necessary for agricultural activities
3. Create and implement assessment tools and procedures to measure learning outcomes
for technical expertise and production.

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Chem.2- General Biochemistry. January 2021
 GENERAL BIOCHEMISTRY
CHEM. 2

Course Overview
Hello and welcome to Biochemistry! This course covers the fundamental aspects
of biochemistry and the structure and dynamics of important cellular components. It
deals with the properties and metabolism of carbohydrates, lipids, proteins and other im-
portant biochemical compounds. This course is also designed to develop techniques and
skills in qualitative and quantitative tests on carbohydrates, proteins, lipids and nucleic
acids.
Biochemistry is an intensive, challenging course as it encompasses many areas
of chemistry and biology. Hence, you are assumed to have prior knowledge in biology,
general chemistry and organic chemistry to better grasp the concepts presented in the
following four (4) modules covered in this course, namely;
Module 1: Fundamentals of Biochemistry
Module 2: Carbohydrates
Module 3: Lipids
Module 4: Proteins and Nucleic acids
The lessons in each module are brief but packed with figures, short activities
and assessments to supplement and evaluate learning. Each lesson has the following
parts and corresponding icons:
This will give you an idea of what you need to acquire
after completing each lesson.
This task is given before starting each lesson. It aims
to test what you knew about the topic.
This can be a question or two that serves as motivation
to build up your interest on the lesson.
This section provides the discussion of the lessons
and aims to help you discover and comprehend the
concepts you have to learn.
This provides you the link to additional readings or
video clips to learn more about the topics.
This task will help you transfer or apply your new
knowledge or skill.
This is an assessment of your level of mastery in
achieving the intended learning outcomes

This provides the list of references used in the module.

At the end of this course, students must be able to:

 demonstrate comprehensive knowledge on the cellular structures and
biochemical compounds by constructing three dimensional models.
 exhibit skills in performing qualitative and quantitative tests on biomolecules.
Students, the more effort you put into this learning material, the more rewarding your
effort will be. Yes, this course is indeed challenging, but definitely interesting and worth the
challenge!
Enjoy and have fun. Happy learning!

DEMEIAPE VERAS BAGALAY iii

Chem.2- General Biochemistry. January 2021
 Module 1 FUNDAMENTALS OF BIOCHEMISTRY

INTRODUCTION

Welcome to your first module, the fundamental concepts in Biochemistry!

The lessons discussed in this module are intended to provide a concrete basic
knowledge in studying the chemistry of life. The module begins with an overview and
history of Biochemistry, and its relevance to other sciences and medicine, which will surely
.
make you realize the remarkable impact of biochemistry into our daily lives.
Biochemistry is a combined biology and chemistry. It is fitting to review your
knowledge in biomolecules and cells. These lessons are discussed for you to better
comprehend how the structure and functions of a cell and its organelles are influenced by
their chemical composition. Take note that the main focus of Biochemistry is to give
understanding how biological molecules give rise to the processes that occur within living
cells and whole organisms.
In this learning module the following lessons will be tackled ;

Lesson 1 Introduction to Biochemistry

1.1 Overview and History of Biochemistry
1.2 Scope and Significance of Biochemistry
1.3 Interrelation of Biochemistry with other fields of science
Lesson 2 Chemical Foundations of Biochemistry
2.1 Elements essential in the life of most organisms
2.2 Overview of the Biomolecules
Lesson 3 Cellular Foundation of Biochemistry
3.1 Cell structure and function
3.2 Major chemical components of cell parts

Upon completing this module, you are expected to;

 define Biochemistry and describe its scope, significance and relationship
with other sciences;
 name and describe the functions of biomolecules in a living system;
 draw, label the parts and describe the functions of a cell; and
 relate the properties of biomolecules to the structure and functions of
organelles and the cell as a whole.
Are you ready? Together, let‘s take the challenge and begin the journey in
learning Biochemistry!

DEMEIAPE VERAS BAGALAY iv

Chem.2- General Biochemistry. January 2021
 Lesson 1 Introduction to Biochemistry Module 1

At the end of this lesson, you are expected to :

a. manifest understanding on definition, history and scope of Biochemistry;
b. distinguish and relate Biochemistry with other sciences;
c. describe common tools and equipment employed in Biochemistry; and
d. recognize the impact and importance of Biochemistry to humankind.

List at least ten (10) things you know about the subject biochemistry.












Why is it so important to study Biochemistry?

_______________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________

1.1. Overview and History of Biochemistry

What comes first in your mind when you encounter the word Biochemistry? It is Biology?
It is Chemistry? Well, Biochemistry is also known as ―biological chemistry‖ or ―physiological
chemistry‖. It is the science that deals with the chemical basis of life, a study of chemical
processes in living organisms. To elaborate, it is a branch of chemistry which deals with the study
of life at the molecular level and the processes associated with life, such as reproduction, growth,
and respiration. Meaning, it is the study of the chemical substances and processes that occur in
plants, animals and microorganisms. When did this science begin?
1650 – 1780 ―Chemistry as a pure science‖
Robert Boyle studied on composition of substances
John Mayow studied on analogy of animal respiration and oxidation of organic
matter in air
Antoine-Laurent Lavoisier (Father of Modern Chemistry) discovered the similarity
of chemical oxidation and respiratory process. He proposed that the combustion
of a candle is similar to the respiration of animals, as both need O 2
Late 18th century: Joseph Priestley, Jan Ingenhousz, Jean Senebier conducted
experiments which lead to conclusion that photosynthesis is a reverse of
respiration

DEMEIAPE VERAS BAGALAY 1

Chem. 2 - General Biochemistry. January 2021
 Lesson 1 Introduction to Biochemistry Module 1

Until early 1800’s: ―vitalism‖ belief: the compounds found in living organisms (e.g.,
organic molecules) can only be produced by living organisms and could not be
produced in the laboratory.
1828: Friedrich Wöhler disproved vitalism and synthesized urea from inorganic matter
(lead cyanate & ammonia)
1838: The term ―protein‖ was first used.
1850’s-1890’s: Carbohydrates, lipids and nucleic acids were recognized.
1877: Louis Pasteur (Father of Microbiology) experimented on fermentation
1897 Eduard and Hans Buchner showed that dead cell extracts can perform reactions
of living cells. The molecules responsible for performing these reactions are
called enzymes
Late 1800's : Emil Fischer on the key/lock picture; Substrate (Key), Enzyme (Lock)
Early 1900's: The field of biochemistry emerged; there were more studies on structure
and function of enzymes; and enzymatic pathways were elucidated
1903: Carl Neuberg introduced the term Biochemistry
1926: James Summer discovered the protein nature of enzyme
Embden & Meyerhof illustrated Glycolytic pathway
1929: ATP was isolated from muscle
1930-1940: Krebs illustrated Citric Acid and Urea Cycles
1940: F.A. Lipmann explained the central role of ATP
1944: It was found out that genes composed of DNA
1953: Watson and Crick determine the structure of DNA
Biological function linked to the information in genes
1953-1977: Frederick Sanger’s worked on sequencing of protein; nucleic acid
1956: Korenberg had discovery of DNA polymerase
1980: Snell et al. worked on recombinant DNA research
20th century : Chemical analysis, separation methods, electronic instrumentation for
biological studies ( X-ray diffraction, electron microscope, and more.
1.2. Scope and Significance of Biochemistry
Biochemistry encompasses the following:
 chemical nature of living organisms;
 relationship of the living organisms to their environment through exchange of
chemical substances;
 processes by which absorbed materials are utilized for synthetic reactions;
 metabolic breakdown of the materials to supply energy; and
 mechanisms which regulate with precision all these processes.
Biochemistry is very important in the field of medicine, agriculture, pharmacy, and
nutrition.
Medicine
a. Physiology : it helps one understand the biochemical changes and related
physiological alteration in the body.
b. Pathology : based on the symptoms described by the patient, physician can get
clue on the biochemical change and the associated disorder.
c. Nursing and diagnosis : in nursing, importance of clinical biochemistry is
invaluable. So the diagnosis of any clinical condition is easily possible by bio-
chemical estimations.

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Chem. 2 - General Biochemistry. January 2021
 Lesson 1 Introduction to Biochemistry Module 1

Agriculture
a. Prevent diseases and Enhance Yield/growth : It helps for prevention, treatment of
diseases and also increase the production or yield.
b. Adulteration : determination even of the composition of food material produced,
for food safety
c. Biochemical tests for the pesticides residues or other toxic waste in plant, food
grain and soil can be evaluated.
d. In animal husbandry : the quality of milk can be checked by biochemical tests.
e. In fisheries : the water quality is regularly monitored by biochemical tests.
f. In plant/ Botany : biochemistry of plants gave way to breakthrough of how food is
synthesized in them and the reason why autotrophs are not dependent on other
living organisms for food.
Pharmacy
a. Drug constitution : biochemistry gives an idea of the constitution of the drug, its
chances of degradation with varying temperature, etc.
b. The half-life and Drug storage : this is a test done on biochemical drugs to know
how long a drug is stable when kept at so and so temperature.
c. Drug metabolism : it also gives an idea of how drug molecules are metabolized by
many biochemical reactions in presence of enzymes.
Nutrition
a. Food chemistry : gives an idea of what we eat.
b. Role of nutrients : due to biochemistry the importance of vitamins, minerals,
essential fatty acids, their contribution to health were known.
c. Physician can prescribe to limit usage of certain food like excess sugar for
diabetics, excess oil for heart and lung problem prone patients, and many more.
1.3. Interrelation of Biochemistry with other fields of science
Biochemistry covers a range of scientific disciplines, including both organic and inorganic
chemistry, physical chemistry, genetics, microbiology, cell biology, molecular biology, physiology,
forensics, plant science, agriculture, and medicine. Among these disciplines, biochemistry is closely
related to molecular biology, the study of molecular mechanisms by which genetic information
encoded in DNA is able to result in the processes of life (fig. 1).

Function
try

Ge
s
hemi

net
ics
Bioc

Proteins Genes
Molecular Biology

Figure 1. Close relationship of Biochemistry to Molecular Biology and Genetics. Source: https://tinyurl.com/y3pp5fk7

In this module, we will not deal with the other sciences interrelated with Biochemistry. So,
don‘t worry. To further elaborate the topics tackled in this lesson, visit the links listed below.

 Introduction to Biochemistry @ https://tinyurl.com/y5p8a4jt

 History and development of Biochemistry@ https://tinyurl.com/y68bhop9
 Introduction to Biochemistry Laboratory Equipments and Safety Measures
@ https://tinyurl.com/y5x2u93j

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Chem. 2 - General Biochemistry. January 2021
 Lesson 1 Introduction to Biochemistry Module 1

ACTIVITY 1
Common Laboratory Tools
And Equipment Used In Biochemistry

INTRODUCTION:
The aims of biochemical research are complex and diverse. Investigation of the network of
chemical reactions taking place in living organisms and representing the most fundamental
phenomena of life, identification of the molecules playing roles in biochemical processes,
determination of their structure, function and interactions, examination of the molecular background
of metabolism, the flow of energy and information within organisms are all among the common
goals of biochemists and molecular biologists. In accordance with this diversity of problems, a high
variety of tools, instruments and methods are required to answer scientific questions effectively.

OBJECTIVES:
At the end of this activity, you will be able to;
a. identify the functions of most common tools and instruments used in Biochemistry;
b. draw these instruments;
c. determine the guidelines in preparing, handling, and storing biological samples and other
chemical substances in a laboratory; and
d. apply the guidelines in proper handling of laboratory apparatus and equipment.

MATERIALS:
ballpen, pencil, eraser, ruler, bond paper, reference books, computer/cell phone,
internet connection

PROCEDURES:
1. Due to pandemic brought about by COVID-19, conduct of actual laboratory activities are
impossible. In this case, you can accomplish this activity by referring to books or information
from reliable on-line resources.
2. Research on the common laboratory tools and equipment used in Biochemistry.
3. Categorize the laboratory tools and equipment according to their uses. Be guided of the table
provided under results and observation.
4. Draw the laboratory tools and equipment with the use of pencil. Use only black or blue ball pen
in writing.
5. Describe the functions of most common tools and instruments used in Biochemistry. Write your
results and observations, analysis and conclusion on the laboratory report sheets,
provided on the next pages.

Note: Only submit the report sheets.

REFERENCES:
Harvey, R. A., & Ferrier, D. R. (2011). Lippincott's Illustrated Reviews: Biochemistry.
Philadelphia: Lippincott Williams & Wilkins.
Hegyi, G., Kardos, J., & Kovacs, M. (2013). Introduction to Practical Biochemistry. Eotvos
Lorand University.
Leningher, A. (2013). Principles of Biochemistry. W.H. Freeman & Company.

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Chem. 2 - General Biochemistry. January 2021
 Lesson 1 Introduction to Biochemistry Module 1

ACTIVITY 1 REPORT SHEET (1/6)

Name: Date performed :

Section: Date submitted :
Lab. Instructor : Rating :

ACTIVITY 1
Common Laboratory Tools
and Equipment used in Biochemistry

RESULTS and OBSERVATIONS:

Common Laboratory Tools and Equipment in Biochemistry:

Name of apparatus/
Drawing Function
equipment
A. Plastic and glass wares used for the storage of liquids:
1.

2.

3.

4.

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Chem. 2 - General Biochemistry. January 2021
 Lesson 1 Introduction to Biochemistry Module 1

ACTIVITY 1 REPORT SHEET (2/6)

Name: Date performed :

Section: Date submitted :
Lab. Instructor : Rating :

ACTIVITY 1
Common Laboratory Tools
and Equipment used in Biochemistry

RESULTS and OBSERVATIONS:

Common Laboratory Tools and Equipment in Biochemistry:

Name of apparatus/
Drawing Function
equipment
B. Tools/glass wares used for mixing of liquids :
1.

2.

3.

4.

DEMEIAPE VERAS BAGALAY 6

Chem. 2 - General Biochemistry. January 2021
 Lesson 1 Introduction to Biochemistry Module 1

ACTIVITY 1 REPORT SHEET (3/6)

Name: Date performed :

Section: Date submitted :
Lab. Instructor : Rating :

ACTIVITY 1
Common Laboratory Tools
and Equipment used in Biochemistry

RESULTS and OBSERVATIONS:

Common Laboratory Tools and Equipment in Biochemistry:

Name of apparatus/
Drawing Function
equipment
C. Equipment used to measure volume :
1.

2.

3.

D. Equipment used to measure mass :

1.

2.

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Chem. 2 - General Biochemistry. January 2021
 Lesson 1 Introduction to Biochemistry Module 1

ACTIVITY 1 REPORT SHEET (4/6)

Name: Date performed :

Section: Date submitted :
Lab. Instructor : Rating :

ACTIVITY 1
Common Laboratory Tools
and Equipment used in Biochemistry

RESULTS and OBSERVATIONS:

Common Laboratory Tools and Equipment in Biochemistry:

Name of apparatus/
Drawing Function
equipment
E. Cooking/Heating apparatus
1.

2.

3.

4.

5.

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Chem. 2 - General Biochemistry. January 2021
 Lesson 1 Introduction to Biochemistry Module 1

ACTIVITY 1 REPORT SHEET (5/6)

Name: Date performed :

Section: Date submitted :
Lab. Instructor : Rating :

ACTIVITY 1
Common Laboratory Tools
and Equipment used in Biochemistry

RESULTS and OBSERVATIONS:

Common Laboratory Tools and Equipment in Biochemistry:

Name of apparatus/
Drawing Function
equipment
G. Other apparatus used in preparation of samples/specimen:
1.

2.

3.

4.

5.

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Chem. 2 - General Biochemistry. January 2021
 Lesson 1 Introduction to Biochemistry Module 1

ACTIVITY 1 REPORT SHEET (6/6)

Name: Date performed :

Section: Date submitted :
Lab. Instructor : Rating :

ACTIVITY 1
Common Laboratory Tools
and Equipment used in Biochemistry

ANALYSIS:
1. Why do you think a variety of laboratory tools and equipment is necessary in Biochemistry?
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________

2. How will you handle biological samples and chemical substances in the laboratory? Suggest
guidelines on handling biological and chemical samples in the laboratory.
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________

3. What are the guidelines or safety measures in handling and taking care of laboratory apparatus
and equipment?
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________

CONCLUSION:
_______________________________________________________________________________
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_______________________________________________________________________________
_______________________________________________________________________________

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Chem. 2 - General Biochemistry. January 2021
 Lesson 1 Introduction to Biochemistry Module 1

Name: Rating:
Section: Date:
Subject Instructor:

Figure 2. Nutrition facts. Source: Nutrition facts of Tipco(DelMonte), Starbucks & Nestle products.

Are you familiar with the pictures above? Yes! Nutrition facts.

1. Are these pictures related/connected to the study of biochemistry? Explain your answer with a
maximum of three sentences.

______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________

2. What could be the greatest impact of Biochemistry to you? To the humankind?

______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________

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Chem. 2 - General Biochemistry. January 2021
Lesson 2 Chemical Foundations of Biochemistry Module 1

At the end of this lesson, you are expected to :

a. describe the roles of the biological elements in chemical processes of cells ;
b. identify biomolecules and their functions in living system; and
c. give the importance of recognizing biomolecules present in organisms.

Pictures below (figure 3) are foods and drinks that contained the four major biomolecules
-carbohydrates, lipids, proteins, and nucleic acids . Identify the biomolecule each of these food
mainly contains.
A B C D

Figure 3. Selected foods and drinks. Sources: (a) tasteofhome.com (b)lifeloveandsugar.com

(c)nippon.com (d)thegheespot.net

What is it in biomolecules? Why are these biomolecules so important in the study of

Biochemistry?
_______________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________

2.1. Elements essential in the life of most organisms

In your previous chemistry subjects, you were taught about elements in the periodic table.
Do you know which of those elements are commonly found in organisms?

In a living cell, 96% of cell cytoplasm are composed of C, H, O and N ; 3% are P, K,

and S; and 1% is composed of Ca, Fe, Mg, Na, Cl, Cu, Mn, Co, Zn and other trace elements
(Bidlack, et al., 2018)

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Chem. 2 - General Biochemistry. January 2021
Lesson 2 Chemical Foundations of Biochemistry Module 1

The figure below shows the bulk and trace elements found in animals.
Fig. 4. Elements essential to animal life and
health. Bulk elements (shaded light red) are
structural components of cells and tissues and
are required in the diet in gram quantities daily.
For trace elements (shaded yellow), the re-
quirements are much smaller: for humans, a
few milligrams per day of Fe, Cu, and Zn,
even less of the others. The elemental require-
ments for plants and microorganisms are simi-
lar to those shown here; the ways in which they
acquire these elements vary. © 2017 Nelson,
D.L., et. al. W.H. Freeman & Co.

In most organisms, the following elements play essential roles in the biological processes in
cells.
Table 1. Elements essential in the life of most organisms
Elements Biological roles
97% of the weight of most organisms; main
hydrogen, oxygen, carbon, nitrogen,
components of macromolecules
zinc, iron, manganese, copper, and
required for life, primarily as cofactors in proteins
cobalt
calcium, chlorine, magnesium, form essential ions which play key roles in cell
potassium, and sodium signaling and neurophysiology

Interactions of these elements through different types of chemical bonding results in the
formation of various molecules and compounds (organic and inorganic) which are very important in
the structures and functions of cells and its organelles, and the characteristics of organisms.
In this learning material, we will only deal with some biomolecules.
2.2. Overview of the Biomolecules
Biological molecules or biomolecules are compounds found within living cells. These
include compounds that are composed mainly of carbon, hydrogen, oxygen, and sometimes
nitrogen, sulfur and phosphorus. They are the building blocks of life and perform important functions
in living organisms. They have a wide range of sizes and structures and perform a vast arrays of
functions. Most biomolecules are organic compounds and can be extremely complex, they are
called biological macromolecules. These are carbohydrates, lipids, proteins and nucleic acids.
Water, an inorganic compound is considered a biomolecule because of its life-supporting properties.
Thus, it is also included in this lesson.
2.2.1.Water and its life-supporting properties

Water is the most important and the most abundant among inorganic compounds making
up 70% or more of the weight of most organisms. It is a highly asymmetric molecule with the
oxygen atom at one end and the two hydrogen atoms at the opposite end (figure 5a). Each of the
two covalent bonds in the molecule is highly polarized, and all three atoms in a water molecule are
adept at forming hydrogen bonds (figure 5b).

Figure 5. Structure of the water molecule. (a) The

dipolar nature of the H2O molecule; the dashed lines repre-
sent the nonbonding orbitals. There is a nearly tetrahedral
arrangement of the outer shell electron pairs around the
oxygen atom; the two hydrogen atoms have localized
partial positive charges (δ+) and the oxygen atom has a
partial negative charge (δ−). (b) Two H2O molecules joined
by a hydrogen bond (three blue lines) between the oxygen
atom of the upper molecule and a hydrogen atom of the
lower one. Hydrogen bonds are longer and weaker than
covalent O—H bonds. © 2017 Nelson, D.L., et. al. W.H.
Freeman & Co.

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Chem. 2 - General Biochemistry. January 2021
Lesson 2 Chemical Foundations of Biochemistry Module 1

The molecular structure of H2O explains many of its unusual properties. The polarity of its
structure allows it to participate in hydrogen bonding which is responsible for the unique properties
such as;
 cohesion: attraction between and among water molecules
 adhesion : ability to adhere on other surface
 high surface tension: results in the cohesion-adhesion property; ability to resist
external forces as the molecules stick together.
 higher melting point, boiling point, and heat of vaporization: there is a need for
more energy to break the strong covalent bonds within water molecules. Meaning,
higher energy is needed for water transform from one state to another.
 universal solvent : water forms hydrogen bonds with other polar molecules (figure
6) and dissolves most of the organic substances.
: Extended networks of hydrogen-bonded water molecules also form
bridges between solutes for example proteins and nucleic acids, that allow the
larger molecules to interact with each other over distances of several nanometers
without physically touching.
: water interacts electrostatically with charged solutes forming ions.
(ionization) as shown in figure 7.

Figure 6. Water as solvent. Water dissolves many

crystalline salts by hydrating their component ions.
The NaCl crystal lattice is disrupted as water mole-
cules cluster about the Cl− and Na+ ions. The ionic
charges are partially neutralized, and the electrostatic
attractions necessary for lattice formation are
weakened © 2017 Nelson, D.L., et. al. W.H. Freeman
& Co.

Figure 7. Common hydrogen bonds in biological

systems. This figure also shows how water interacts
with other polar and charged molecules through
hydrogen bonding. © 2017 Nelson, D.L., et. al. W.H.
Freeman & Co.

Why is water an important factor in cells? Because it is able to form weak interactions with
so many different types of chemical groups. Remember, water molecules form H-bonds with organic
molecules that contain polar groups (e.g. sugars, larger molecules) hence, polar molecules and ionic
compounds are soluble within the cell.
2.2.2. Biological Macromolecules

Carbohydrates, lipids, proteins and nucleic acids are large and complex biomolecules
composed of monomers (building blocks) linked together to create large macromolecules, which are
known as polymers. These polymers are mainly composed of the macroelements C, H, O, N and P.
Carbohydrates – (CH2O)n
Lipids - CHO
Proteins - CHON
Nucleic acids - CHONP
A process whereby monomers are linked together to synthesize a biological polymer is
called “dehydration synthesis or condensation”. This process involves the removal of water to form a
bond that connects monomers together. Let‘s have a brief introduction of these large biomolecules.

Carbohydrates
We often referred carbohydrates as carbs! Actually, they are sugars! They are made up of
monosaccharide monomers, the simple sugars. These molecules are good and quick sources of
energy. Where can we get these carbs? Starchy foods like rice, bread, cakes, crop roots are just few
of the many examples.

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Chem. 2 - General Biochemistry. January 2021
Lesson 2 Chemical Foundations of Biochemistry Module 1

Lipids
Lipids are better known as fats and they have two different types of monomers. One is
called fatty acids and the other one is glycerol. Food sources of lipids include butter, oil and
cholesterol. You might avoid these foods, but they can serve a lot of great functions in your body. To
name some, fats are great sources of long stored energy and lipids make up the cell membranes.
But, we must be aware that excessive amount of lipids could be a bad thing to our health. It‘s all
about moderation.
Proteins
What is in your mind when you hear about proteins? You might think about muscle building.
Well, correct! Protein is great for muscle building. These molecules are called the building blocks of
cells and tissues. They are made up of amino acids. So if you see in your food label that it is rich in
amino acids, it is good for muscle building. But, that‘s not the only function of proteins. Proteins
serve other functions such as working in immune system and acting as enzymes. Where to get
these proteins? Take all sorts of meat, fish, eggs, milk, are legumes.
Nucleic acids
There are two types of nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid
(RNA). They are both made of nucleotides. These nucleotides are composed of five-carbon sugar,
nitrogenous bases and a phosphate. They can be found in lots of your foods because whenever you
eat something that once living contain these molecules. For example, eating a banana is consuming
all its cells which contain nucleic acids DNA and RNA in the nucleus and RNA in the cytoplasm.
These nucleic acids perform their functions in gene expression. DNA directs cell activities and RNA
plays its main role in protein synthesis, the translation of genetic information.
More about these four complex biomolecules are discussed in the next modules. Watch the
video from the link below to learn more about biomolecules.

Watch: 1. Biomolecules @ https://tinyurl.com/z2dqdsv

2. Macromolecules @ https://tinyurl.com/y4urou5d

ACTIVITY 2
What’s in my favorite foods?

INTRODUCTION:
Living things acquire nutrition in any means to sustain metabolism. Like other forms of
animals, we humans take in foods to supply the energy requirements for our daily activities. Each
of us obviously has different preferences of foods we eat depending on the satisfaction of our taste
buds! But, are we considering what we can get from our preferred foods?

OBJECTIVES:
At the end of this activity, you will be able to;
1. identify the biomolecules present in your favorite foods; and
2. decide some adjustments in your food preferences.
MATERIALS: ballpen, ruler, reference books, computer/cell phone, internet connection
PROCEDURES:
1. List down 10 of your favorite foods and drinks and identify if it is high in sugars, fats, amino
acids or nucleic acids. Describe the possible health effects of the foods.
2. Make a new list of foods if you decide to make changes to your previous list for healthier diet.
3. Write your answers under results and observations. Also, do the analysis and conclusion on
the activity report sheets provided on the next pages. Only submit the report sheets.

REFERENCE: ( 2021 course pack of Compostela Valley State College)

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Chem. 2 - General Biochemistry. January 2021
Lesson 2 Chemical Foundations of Biochemistry Module 1

ACTIVITY 2 REPORT SHEET (1/2)

Name: Date performed :

Section: Date submitted :
Lab. Instructor : Rating :

ACTIVITY 2
What’s in my favorite foods?

RESULTS and OBSERVATIONS:

A. What can I get from my favorite foods and drinks?

Favorite foods
Abundant Monomers present Possible effects to health
(start form the most favorite)

1.

2.

3.

4.

5.

6.

7.

8.

9.

10.

B. My new list of favorite foods for healthier diet.

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Chem. 2 - General Biochemistry. January 2021
Lesson 2 Chemical Foundations of Biochemistry Module 1

ACTIVITY 2 REPORT SHEET (2/2)

Name: Date performed :

Section: Date submitted :
Lab. Instructor : Rating :

ACTIVITY 2
What’s in my favorite foods?

ANALYSIS:

1. Why is it important to observe healthy diet?

_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________

2. Explain what is meant by ― you are what you eat‖?

_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________

CONCLUSION:

_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________
______________________________________________________________________________

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Chem. 2 - General Biochemistry. January 2021
Lesson 2 Chemical Foundations of Biochemistry Module 1

Name: Rating:
Section: Date:
Subject Instructor:

Answer the following questions with a maximum of five sentences:

1. How is a chemical element similar to a building block?

2. Why is hydrogen bonding important in biological system?

3. Is it important to be able to recognize the biomolecules in living organisms? Yes or No? Why?

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Chem. 2 - General Biochemistry. January 2021
 Lesson 3 Cellular Foundation of Biochemistry Module 1

At the end of this lesson, you are expected to :

a. diagram cells and label the parts.
b. identify the biomolecule components of cell parts; and
c. explain how the functions of each cellular structure are influenced by the
biomolecule components.

Put a check if organelles/cell parts are present in bacterial, plant cell or in animal cell.

Organelles Bacterial Cell Animal cell Plant cell

Cell wall
Plasma membrane
Cytoplasm
Nucleus
Chromosomes
Centrosome
plasmid
Golgi apparatus
Endoplasmic reticulum
mitochondrion
Central vacuole
cilia
Flagellum
Lysosomes

Do you agree that all living organisms manifest the life properties of cells? What are the
life attributes of cells that are related to organisms?
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________
______________________________________________________________________________

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Chem. 2- General Biochemistry. January 2021
 Lesson 3 Cellular Foundation of Biochemistry Module 1

3.1. What are cells?

In biology, cell is the basic membrane-bound unit that contains the fundamental
molecules of life and of which all living things are composed of. Every human individual is
composed of more than 30, 000, 000, 000, 000 cells.
In the modern cell theory. The cell is the smallest living unit in all organisms. Second, that
all of living organisms are made of cells. Third, all cells come from other pre-existing cells.
Do you know that cells have their own little world inside them. They carry genetic
information (DNA) which dictates all cell activities, they can divide, and perform complex but
coordinated functions and life processes carry out by the different organelles and cell parts for the
life of the entire cell or organism.
3.1.1 Types of cells

Cells are classified based on the presence of nucleus:

1. Prokaryotic (―pro‖ means before; ―karyon” means nucleus) .These are cells without
nucleus and membrane-bound organelles. An example of this cell type is bacterial cell.
2. Eukaryotic (“eu” means true or good; “karyon” means nucleus). These are cells with true
nucleus and membrane-bound organelles like the cells of animals, plants, fungi and
protists.
Organisms are classified based on the type of cells they are composed of:

1. Prokaryotes is the term referred to organisms made up of prokaryotic cells. The typical
example of prokaryotes are the bacteria or organisms that belong to Kingdom Eubacteria
and Archaea.
2. Eukaryotes on the other hand refers to organisms made up of eukaryotic cells. Animals,
fungi plants and members of kingdom Protista are eukaryotes.

Table 2. Cellular Structures in Prokaryotic and Eukaryotic Cells

Eukaryotic Cells
Cell Part/organelle Prokaryotic Cell
Animal Plant
Capsule present absent absent
present present (one; male
Flagellum generally absent
(one or more) gamete)
present present
Cell wall absent
(made of peptidoglycan) (made of cellulose)
Nucleus absent present present
present present (double he- present
Chromosome
(one & circular) lix) (double helix)
Endoplasmic reticu-
absent present present
lum
Golgi apparatus absent present present
Mitochondrion absent present (more) present (less)
Chloroplast absent absent present
usually absent; if pre- present
vacuole absent
sent, small but more (large central vacuole)
Lysosome absent present rare/absent
Peroxisome absent present present

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Chem. 2- General Biochemistry. January 2021
 Lesson 3 Cellular Foundation of Biochemistry Module 1

3.1.2. Functions of the Cell Parts and Organelles

Let us familiarize some frequently encountered terms when studying structures of cells.
 Protoplasm is the living components of the cell. It is surrounded by plasma membrane. It re-
fers to all structures within the plasma membrane.
 Cytoplasm refers to all cellular components between the plasma membrane and the
nucleus. This is the region outside the nucleus but inside plasma membrane.
 cytosol is the soup-like fluid within cytoplasm where various organelles are suspended.
 organelles or ‗‗little organs‖ refer to the membrane-bound and the non-membrane bound
structures within the cell. Some examples are nucleus, mitochondrion, chloroplast, and
ribosomes.

Table 3. Functions of Cellular Structures

Cellular Structures Description and Function

bounded by nuclear envelope, that separates nucleus from cytoplasm.
Has nuclear pores in the nuclear membranes permit only certain kinds of mole-
cules (for example, proteins being carried into the nucleus and RNA being car-
ried out) to pass between the nucleus and the cytoplasm. Inside the nucleus are:
Nucleus
nucleoplasm, the granular-appearing fluid, chromatin and nucleolus, containing
the RNA and associated proteins. This is where ribosomes are made.
acts as the control center of the cell and directs all cellular activities because
it contains the DNA.
Non-membrane bound tiny bodies with two subunits that are composed of RNA
Ribosome and proteins; considered the protein manufacturers ;also found attached to ER
or scattered in the cytoplasm
attached to the nuclear membrane. Structurally, it is an enclosed space consist-
ing of a network of flattened sacs and tubes that form channels throughout the
Endoplasmic reticulum
cytoplasm . Can be rough ( with ribosomes-involved in protein synthesis, secre-
(ER)
tion and storage) or smooth (without ribosomes-involved in carbohydrate and
lipid synthesis )
stacks of flattened discs or vesicles often bounded by branching tubules that
originate from the endoplasmic reticulum but are not directly connected to
Golgi Apparatus/
it . they are called the collecting, packaging, and delivery centers or, as ―post
dictyosomes
offices‖ of the cell; modification of carbohydrates and proteins synthesized and
packaged in ER
Chloroplast Photosynthetic apparatus which contains the green pigment chlorophyll needed
for photosynthesis
Mitochondrion powerhouses of the cell; double membrane organelle shaped like cucumbers,
paddles, rods, or balls.
cytoskeleton intricate network constructed mainly of two kinds of fibers; microtubules (―hollow
tubes‖) and microfilaments; skeletal system of the cell‖ ; involved in cell division;
play a major role in the contraction and movement of cells
Vacuoles act as the storage of materials. (plant cells contain large central vacuole while
animal cells may have none to several small vacuoles)
Cell membrane A bilayer of phospholipids which act as the semi-permeable barrier that controls
what gets in or out of the cell.

There more of the cell organelles not mentioned and described here. You may want to
review your previous lessons in Botany or Zoology.

3.2. Major chemical components of the cell parts

Structure and function of a cell is influenced by its chemical components. The next
table shows the major biomolecules, their function and location in a cell. Hopefully, you will be able
to connect the relationship of biomolecules and the properties of cells.

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Chem. 2- General Biochemistry. January 2021
 Lesson 3 Cellular Foundation of Biochemistry Module 1

Table 4. The Biomolecule and their function in cells

Location in the
Biomolecule Properties Examples Functions
cell
Carbohy- Made of C, H, O Monosaccharides Chloroplast primarily act as
drates 1C:2H:1O ratio Glucose, galactose, Mitochondrion energy source and
(often called General formula of C fructose Cytoplasm storage
glycans) (H2O) Can be triose help mediate spe-
Plasma mem-
One molecule of wa- (3C);pentose (5C); brane cific interactions of
ter in every atom of hexose (6C) based on a cell with its sur-
carbon number of C atoms roundings
Made up of monosac- Disaccharides serve as durable
charide monomers Maltose, sucrose, biological structural
Generally sugars and lactose material support
starches especially in plant
Polysaccharides cells
Most abundant in na- Plastid
ture Starch, glycogen, Cytoplasm
cellulose, chitin Cell wall
Proteins Made of C, H, O, N Messenger, transport, Cell membrane, Cell transport and
Sometimes with S receptor proteins ribosomes, vesi- communication
Made of amino acid cles, endoplas- Cellular structure
Defense proteins
monomers that usually mic reticulum, and support
(antibodies)
form polypeptide golgi apparatus Immunity
chains Structural proteins Cell surface Regulate chemical
reactions
Enzymes Throughout cell

Nucleic Made of C, H, O, N, P Deoxyribonucleic Acid Nucleus, Store genetic infor-

Acids Composed of nucleo- (DNA) chloroplast, mation
tide monomers mitochondrion
Each nucleotide con-
sists of:
5-carbon sugar
>deoxyribose (in DNA)
>ribose (in RNA)
Nitrogen bases
>guanine (G), adenine
(A), cytosine (C), thy-
mine (T) (in DNA)
Ribonucleic Acid Nucleolus, Decode genetic in-
>guanine (G), adenine
(RNA) cytoplasm, formation for protein
(A), cytosine (C), uracil
ribosome synthesis
(U) (in RNA)
Phosphate group
Lipids Made of C, H, O Fats and oils Cytoplasm serve as long term
with less oxygen waxes Cell surface energy reserve
sometimes with P Phospholipids (cutin, suberin) Protection
Composed of a unit of Steroids  major structural
glycerol or other Cell membrane components of cell
alcohol with three fatty membranes
acids attached Cell membrane
chemical messen-
Insoluble in water gers (steroid hor-
mones and as cell
surface receptors

Watch: Cell Theory and prokaryotic vs. eukaryotic cells

@ https://tinyurl.com/y2tbnvgx
Read: Protoplasm @ https://tinyurl.com/yxv6hfoj

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Chem. 2- General Biochemistry. January 2021
 Lesson 3 Cellular Foundation of Biochemistry Module 1

ACTIVITY 3
The Cells

INTRODUCTION:

Cells are diverse in structure and differ in functions as influenced by their chemical
components. Both the prokaryotic and eukaryotic cells possessed cell parts that work in
coordination to sustain the life of the cell or entire organism.

OBJECTIVES:
At the end of this activity, you will be able to:
1. draw and label the parts of prokaryotic and eukaryotic cells; and
2. relate the structure of prokaryotic and eukaryotic cells to properties of the whole
organism.

MATERIALS: ballpen, pencil, ruler, reference books, computer/cell phone, internet connection

PROCEDURES:
A.
1. Draw a prokaryotic and eukaryotic cells (plant and animal) using a pencil.
2. Label the parts of the cells in the right side of the paper using ball pen.
3. Write your answers under results and observations. Also, do the analysis and conclusion on
the activity report sheets provided on the next pages. Only submit the report sheets.
B.
1. Choose one among bacteria, an animal and a plant.
2. Craft and present a two-minute video describing the role of its organelles.
3. Explain in that video how the function of each organelle is influenced by its chemical
composition. Your video presentation will be rated based on the following criteria:
Content (accuracy and completeness of information) - 60%
Organization and Presentation of Information - 30%
Timeliness - 10%

4. Send the recorded video or the link of your recorded video to your instructor through FB
messenger.

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Chem. 2- General Biochemistry. January 2021
 Lesson 3 Cellular Foundation of Biochemistry Module 1

ACTIVITY 3 REPORT SHEET (1/2)

Name: Date performed :
Section: Date submitted :
Lab. Instructor : Rating :

ACTIVITY 3
Cells

RESULTS and OBSERVATIONS:

A. Prokaryotic Cell

B. Animal Cell

C. Plant Cell

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Chem. 2- General Biochemistry. January 2021
 Lesson 3 Cellular Foundation of Biochemistry Module 1

ACTIVITY 3 REPORT SHEET (2/2)

Name: Date performed :
Section: Date submitted :
Lab. Instructor : Rating :

ACTIVITY 3
The Cells

ANALYSIS:

1. What are the common cellular structures of the three cells you have drawn?

2. Explain the relation of the unique features of each of the three cells to their distinguishing feature
as organisms.

CONCLUSION:

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Chem. 2- General Biochemistry. January 2021
 Lesson 3 Cellular Foundation of Biochemistry Module 1

Name: Rating:
Section: Date:
Subject: Instructor:

A. Choose and write the letter that corresponds to your answer before each number.
___ 1. Which is not a property of all cells?
a. Cells have DNA in the nucleus c. Cells acquire and use energy
b. Cells evolve d. Cells die
___ 2. Which type of cells has the nucleoid and cell wall as some of its components?
a. Prokaryotic cell c. animal cell
b. Eukaryotic cell d. plant cell
___ 3. Which set of cellular structures is present in prokaryotic cells?
a. Nucleus, ribosomes c. Cell membrane, ribosomes
b. Cell wall, cytoplasm d. ribosome, nucleoid
___ 4. Among the following structures, which one protects the genetic material of eukaryotes?
a. Cell membrane c. nucleiod
b. Nuclear membrane d. Cell wall
___
5. Which of these organelles is responsible for plants‘ photosynthetic nature?
a. central vacuole c. chloroplast
b. cell wall d. dictyosome
___
6. Which set of cellular structures functions for generation of energy for the plant cell?
a. rough ER, dictyosomes
b. ribosomes, central vacuole
c. mitochondria, chloroplast
d. nucleus, mitochondria
___ 7. Which organelle ensures that after cell division each daughter cell has the correct number
of chromosomes ?
a. centriole
b. nucleus
c. ribosomes
d. ribosomes
___
8. Unlike animal cells, plant cells do not have centrioles to initiate formation of spindle fibers
for cell division. What cellular structure in plant cells functions in spindle formation?
a. microbodies
b. microtubules
c. nuclear membrane
___ d. dictyosome
9. In a cell, organelles perform functions in coordination with one another. Which of the
following sets of organelles will be needed so a cell can make and use proteins?
a. nucleus>ribosome>rough ER>dictyosome
b. nucleus>ribosome>rough ER>vesicle
c. nucleus>rough ER>vesicle> dictyosome
d. nucleus>rough ER>ribosome>vesicle
10. Which of the following best supports the statement that nucleus is the control center of a
cell?
a. Nucleus is usually located at the center of the cell.
b. Nucleus is the site for DNA and RNA synthesis
c. It houses the DNA
d. It carries hereditary material

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Chem. 2- General Biochemistry. January 2021
 Module 1 FUNDAMENTALS OF BIOCHEMISTRY

E-Learning, 3. (2017). Illustrated Handbook of Biochemistry. New Year, USA: 3G E-Learning

LLC.

Harvey, R. A., & Ferrier, D. R. (2011). Lippincott's Illustrated Reviews: Biochemistry.

Philadelphia: Lippincott Williams & Wilkins.

Hegyi, G., Kardos, J., & Kovacs, M. (2013). Introduction to Practical Biochemistry. Eotvos
Lorand University.

Larsen, & Keller. (2017). Principles of Biochemistry. (T. Campbell, Ed.) New York, USA: Larsen
& Keller Education.

Leningher, A. (2013). Principles of Biochemistry. W.H. Freeman & Company.

Nelson, D. L., & Cox, M. M. (2017). Lehninger Principles of Biochemistry (7th ed.). New York,
USA: W.H. Freeman and Company

Yutimco, Mac Gerald A. (2021). Chem 14: Biochemistry. Compostela Valley State University.
(Unpublished Course Pack)

Online references:

https://www.britannica.com/science/biochemistry#ref48716
https://www.slideshare.net/HikmetGekil/biochemistry-a-brief-history-of-biochemsitry
https://www.youtube.com/watch?v=CHJsaq2lNjU
https://www.youtube.com/watch?v=RpDx0DVJmeo
https://www.youtube.com/watch?v=BbKi6ExQdxo v=rhTh8LYYBcQ

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Chem.2- General Biochemistry. January 2021